I think part of what is generally expected of us is that we will help prevent AVOIDABLE accidents. Clearly, a Captain electing to "kick", or even "defend a goal" for the opening kick off should trigger a caution flag at any level.
How you choose to deal with that caution is not as important as the fact that you choose to deal with it. Checking with coaches before the coin toss makes sense, as does simply making absolutely sue that the Captain making that choice understands exactly what the consequences of that choice are, and repeating your instructions until he actually does understand. If necessary, and the sense of caution persists, it's not impossible to suggest the player seek guidance (from the coin toss location) from his coach (on the sideline).
Sometimes players just get confused and hopefully we're able to recognize confusion, and within reason, assist the player in calming down, clearly understanding the choices he has available and the consequences of each. When assured confusion is not a factor, at the NFHS level, the Captain is designated to make that selection.
Eliminating the problem is the objective, there are several ways to accomplish that and the important thing is that the way you select, works. What you don't want to do is simply be a passive witness to an AVOIDABLE accident.